research papers
The structure of a new mineral jadarite, LiNaSiB3O7(OH) (IMA mineral 2006–36), has been determined by simulated annealing and Rietveld refinement of laboratory X-ray powder diffraction data. The structure contains a layer of corner-sharing, tetrahedrally coordinated Li, Si and B forming an unbranched vierer single layer, which is decorated with triangular BO3 groups. The Na ion is situated between the tetrahedral layers in a distorted octahedral site. As the very high boron content in this mineral makes obtaining neutron diffraction data very problematic, ab initio optimization using VASP was used to validate the structure and to better localize the H atom. The H atom is located on the apex of the triangular BO3 group and is involved in a weak intralayer hydrogen bond. The final Rietveld refinement agrees with the ab initio optimization with regard to a hydrogen bond between the H atom and one of the tetrahedral corner O atoms. The refined structure seems to be of a remarkably high quality given the complexity of the structure, the high proportion of very light elements and the fact that it was determined from relatively low-resolution laboratory data over a limited 2θ range (10–90° 2θ).
Keywords: powder diffraction; structure determination; mineral structures; simulated annealing; ab initio optimization.
Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108768107010130/lm5008sup1.cif | |
Text file https://doi.org/10.1107/S0108768107010130/lm5008sup2.txt | |
Portable Document Format (PDF) file https://doi.org/10.1107/S0108768107010130/lm5008sup3.pdf |
Computing details top
Data reduction: Topas 4 beta (14/7/2006); program(s) used to solve structure: Topas 4 beta (14/7/2006); program(s) used to refine structure: Topas 4 beta (14/7/2006); molecular graphics: Diamond 3.1d; software used to prepare material for publication: Topas 4 beta (14/7/2006).
(phase) top
Crystal data top
B3HO8Si·Na·Li | V = 594.18 (2) Å3 |
Mr = 219.46 | Z = 4 |
Monoclinic, P21/c | Dx = 2.453 Mg m−3 Dm = 2.453 Mg m−3 Dm measured by Bermann balance |
Hall symbol: -P 2ybc | Cu Kα radiation, λ = 1.5418 Å |
a = 6.7620 (1) Å | µ = 4.51 mm−1 |
b = 13.8016 (3) Å | T = 298 K |
c = 7.6878 (2) Å | , white |
β = 124.089 (1)° | × × mm |
Data collection top
Bruker D8 Advance diffractometer | h = ?→? |
Absorption correction: for a cylinder mounted on the ϕ axis Debye-Scherrer correction | k = ?→? |
Tmin = ?, Tmax = ? | l = ?→? |
Refinement top
Refinement on F2 | 1 constraint |
Least-squares matrix: full | H atoms treated by a mixture of independent and constrained refinement |
S = 1.27 | Unit |
87 parameters | (Δ/σ)max = 0.001 |
Crystal data top
B3HO8Si·Na·Li | V = 594.18 (2) Å3 |
Mr = 219.46 | Z = 4 |
Monoclinic, P21/c | Cu Kα radiation |
a = 6.7620 (1) Å | µ = 4.51 mm−1 |
b = 13.8016 (3) Å | T = 298 K |
c = 7.6878 (2) Å | × × mm |
β = 124.089 (1)° |
Data collection top
Bruker D8 Advance diffractometer | Tmin = ?, Tmax = ? |
Absorption correction: for a cylinder mounted on the ϕ axis Debye-Scherrer correction |
Refinement top
S = 1.27 | H atoms treated by a mixture of independent and constrained refinement |
87 parameters |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
x | y | z | Uiso*/Ueq | ||
Li1 | 0.462 (2) | 0.1995 (6) | 0.1383 (15) | 0.046 (3)* | |
Na1 | 0.9733 (3) | 0.99060 (10) | 0.7544 (3) | 0.0764 | |
B1 | 0.2096 (17) | 0.1602 (8) | 0.6623 (18) | 0.091 (3)* | |
B2 | 0.6920 (14) | 0.3493 (6) | 0.4160 (15) | 0.054 (2)* | |
B3 | 0.5290 (10) | 0.5022 (4) | 0.7860 (9) | 0.0947 | |
Si1 | 0.0378 (4) | 0.7539 (2) | 0.2048 (3) | 0.0584 (5)* | |
O1 | 0.8157 (7) | 0.7241 (3) | 0.9895 (6) | 0.0651 (14)* | |
O2 | 0.2673 (7) | 0.7818 (3) | 0.2102 (6) | 0.0663 (13)* | |
O3 | 0.9733 (6) | 0.8483 (3) | 0.2873 (7) | 0.0581 (14)* | |
O4 | 0.1150 (5) | 0.6584 (3) | 0.3491 (6) | 0.0542 (13)* | |
O5 | 0.7457 (8) | 0.5506 (3) | 0.8761 (9) | 0.0708 (15)* | |
O6 | 0.6846 (9) | 0.4560 (3) | 0.3520 (8) | 0.0570 (13)* | |
O7 | 0.5489 (7) | 0.6725 (3) | 0.6198 (6) | 0.0634 (12)* | |
O8 | 0.5299 (3) | 0.4051 (3) | 0.8362 (6) | 0.0733 (14)* | |
H1 | 0.699 (3) | 0.3993 (14) | 0.936 (3) | 0.0953 (19)* |
Atomic displacement parameters (Å2) top
U11 | U22 | U33 | U12 | U13 | U23 | |
Na1 | 0.091 (6) | 0.0657 (18) | 0.081 (2) | 0.01 (7) | 0.038 (2) | −0.0046 (19) |
B3 | 0.046 (7) | 0.158 (10) | 0.098 (11) | 0.016 (7) | 0.043 (8) | 0.078 (8) |
Geometric parameters (Å, º) top
Li1—O1 | 1.882 (11) | B1—O5 | 1.602 (12) |
Li1—O2 | 1.898 (10) | B2—O2 | 1.479 (12) |
Li1—O8 | 1.957 (11) | B2—O7 | 1.522 (11) |
Li1—O7 | 1.978 (14) | B2—O4 | 1.528 (9) |
Li1—O7 | 2.598 (13) | B2—O6 | 1.544 (10) |
Li1—H1 | 2.36 (2) | B3—O6 | 1.352 (7) |
Na1—O4 | 2.212 (4) | B3—O5 | 1.391 (7) |
Na1—O3 | 2.303 (5) | B3—O8 | 1.394 (7) |
Na1—O5 | 2.477 (6) | Si1—O1 | 1.542 (4) |
Na1—O6 | 2.561 (7) | Si1—O2 | 1.577 (6) |
Na1—H1 | 2.579 (17) | Si1—O4 | 1.611 (5) |
Na1—O6 | 2.624 (5) | Si1—O3 | 1.613 (5) |
Na1—O5 | 2.728 (8) | H1—O8 | 0.960 (15) |
B1—O1 | 1.395 (14) | H1—O3 | 2.155 (14) |
B1—O3 | 1.493 (16) | H1—O5 | 2.20 (2) |
B1—O7 | 1.561 (9) | ||
O1—Li1—O2 | 108.8 (6) | O2—B2—O7 | 109.3 (7) |
O2—Li1—O7 | 103.9 (5) | O2—B2—O4 | 112.4 (6) |
O2—Li1—O8 | 102.1 (5) | O2—B2—O6 | 112.2 (6) |
O8—Li1—O7 | 120.1 (5) | O7—B2—O4 | 108.6 (7) |
O4—Na1—O3 | 150.49 (17) | O6—B3—O5 | 123.3 (6) |
O4—Na1—O5 | 92.43 (15) | O6—B3—O8 | 117.6 (5) |
O4—Na1—O6 | 115.57 (17) | O5—B3—O8 | 119.0 (5) |
O3—Na1—O5 | 94.79 (16) | O1—Si1—O2 | 116.4 (3) |
O3—Na1—O6 | 88.16 (17) | O1—Si1—O4 | 105.4 (2) |
O1—B1—O3 | 122.4 (9) | O1—Si1—O3 | 108.8 (3) |
O1—B1—O7 | 113.2 (8) | O2—Si1—O4 | 104.3 (3) |
O1—B1—O5 | 113.0 (7) | O4—Si1—O3 | 116.5 (3) |
O3—B1—O7 | 104.5 (8) | O8—H1—O3 | 157.2 (17) |
Experimental details
Crystal data | |
Chemical formula | B3HO8Si·Na·Li |
Mr | 219.46 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 298 |
a, b, c (Å) | 6.7620 (1), 13.8016 (3), 7.6878 (2) |
β (°) | 124.089 (1) |
V (Å3) | 594.18 (2) |
Z | 4 |
Radiation type | Cu Kα |
µ (mm−1) | 4.51 |
Crystal size (mm) | × × |
Data collection | |
Diffractometer | Bruker D8 Advance diffractometer |
Absorption correction | For a cylinder mounted on the ϕ axis Debye-Scherrer correction |
No. of measured, independent and observed (?) reflections | ?, ?, ? |
Rint | ? |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | ?, ?, 1.27 |
No. of reflections | ? |
No. of parameters | 87 |
No. of restraints | ? |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | ?, ? |
Computer programs: Topas 4 beta (14/7/2006), Diamond 3.1d.